Nextflow Registry | nf-core/gecco/convert@0.0.0-6c4ed3a

nf-core/gecco/convert @ 0.0.0-6c4ed3a

This command helps transforming the output files created by GECCO into helpful format, should you want to use the results in combination with other tools.

bgc reformatting clusters gbk gff bigslice faa fna

Latest version: 0.0.0-6c4ed3a

Total downloads: 10

Source: nf-core/modules

Authors: @vagkaratzas

Maintainers: @vagkaratzas

Summary

This command helps transforming the output files created by GECCO into helpful format, should you want to use the results in combination with other tools.

Get started

Add the following snippet to your workflow script to include this module.

include { GECCO_CONVERT } from 'nf-core/gecco/convert'

License

MIT License

Process

`Name`	`GECCO_CONVERT`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`clusters` file	TSV file containing coordinates of gecco predicted clusters and BGC types. `*.clusters.tsv`
`gbk` file	Per cluster GenBank file containing sequence with annotations `*.gbk`

`mode` string	Either clusters or gbk folder output, depending on what is reformatted

`format` string	Format for the output file

Output 5 channels

#1 faa tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`${prefix}/*.faa` file	Amino-acid FASTA converted GenBank files of all the proteins in a cluster `*.faa`

#2 fna tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`${prefix}/*.fna` file	Nucleotide sequence FASTA converted GenBank files from the cluster `*.fna`

#3 gff tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`${prefix}/*.gff` file	GFF3 converted cluster tables containing the position and metadata for all the predicted clusters `*.gff`

#4 bigslice tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`${prefix}/.region.gbk` file	Converted and aliased GenBank files so that they can be loaded by BiG-SLiCE `.region.gbk`

#5 versions

`versions.yml` file	File containing software versions `versions.yml`

Tool	Description	Homepage
gecco	Biosynthetic Gene Cluster prediction with Conditional Random Fields.	https://gecco.embl.de

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:20:50 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fgecco%2Fconvert/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gecco/convert/blobs/sha256:6f561f47d70805ba6663380a5fe6b1ccccea1512c953811004f2b0d9c1e84fde
Size	3.1 KB
Checksum	sha256:6f561f47d70805ba6663380a5fe6b1ccccea1512c953811004f2b0d9c1e84fde
Downloads	3

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:20:50 (UTC)	3	3.1 KB
0.0.0-3fc6d40	22 Apr 2026 15:13:35 (UTC)	3	3.1 KB
0.0.0-0c7146d	08 Apr 2026 19:05:15 (UTC)